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IP Watch: Roche, Rubicon, NuGen, Alere, Merck, Gen-Probe, Intel, and Others Win US Patents

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Roche has been awarded US Patent No. 8,071,338, "Suppression of amplification using an oligonucleotide and a polymerase significantly lacking 5'-to-3' nuclease activity."

Nicolas Newton is named as the inventor on the patent.

Provides methods and compositions for amplifying a target sequence by suppressing amplification of related sequences.

Roche has also been awarded US Patent No. 8,071,303, "Reagents and methods for detecting Neisseria gonorrhoeae."

Diane Kawa, Shi-Da Lu, and Peter Dailey are named as inventors on the patent.

Provides compositions and methods for detecting N. gonorrhoeae in a sample. The patent also provides related reaction mixtures, kits, systems, and computers.


Rubicon Genomics has been awarded US Patent No. 8,071,312, "Methods for producing and using stem-loop oligonucleotides."

Vladimir Makarov, Emmanuel Kamberov, and Brendan Tarrier are named as inventors on the patent.

Concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.


NuGen Technologies has been awarded US Patent No. 8,071,311, "Methods and compositions for amplification of RNA sequences."

Nurith Kurn is named as the inventor on the patent.

Provides methods for isothermal amplification of RNA, particularly a plurality of RNA species in a sample. The methods employ a composite primer, a second primer, and strand displacement to generate multiple copies of DNA products comprising sequences complementary to an RNA sequence of interest. In another aspect, the methods employ a single primer (which is a composite primer) and strand displacement to generate multiple copies of DNA products comprising sequences complementary to an RNA sequence of interest. In some embodiments, a transcription step is included to generate multiple copies of sense RNA of an RNA sequence of interest. The methods are useful for preparing nucleic acid libraries and substrates for analysis of gene expression of cells in biological samples. The invention also provides compositions and kits for practicing the amplification methods, as well as methods that use the amplification products.


Alere has been awarded US Patent No. 8,071,308, "Recombinase polymerase amplification."

Olaf Piepenburg, Niall Armes, and Mathew Parker are named as inventors on the patent.

Describes novel, diverse, hybrid, and engineered recombinase enzymes, and the use of such proteins with associated recombination factors for carrying out DNA amplification assays. The invention also features different recombinase systems having distinct biochemical activities in DNA amplification assays; and differing requirements for loading factors, single-stranded DNA-binding proteins; and the quantity of crowding agent employed.


Merck has been awarded US Patent No. 8,071,306, "Methods for quantitating small RNA molecules."

Christopher Raymond is named as inventor on the patent.

In one aspect, the invention provides methods for amplifying a microRNA molecule to produce DNA molecules. The methods include the steps of: (a) using primer extension to make a DNA molecule that is complementary to a target microRNA molecule; and (b) using a universal forward primer and a reverse primer to amplify the DNA molecule to produce amplified DNA molecules. In some embodiments, at least one of the forward primer and the reverse primer comprise at least one locked nucleic acid molecule.


Gen-Probe has been awarded US Patent No. 8,071,301, "Method of isolating nucleic acids from a biological sample."

Kui Gao, Michael Becker, Wen Wu, and Jeffrey Linnen are named as inventors on the patent.

Describes a method of preparing a biological sample appropriate for use in a subsequent in vitro nucleic acid amplification reaction. The method involves a rapid, transient exposure of the sample to alkaline conditions, which can be achieved by mixing an alkaline solution with a pH-buffered solution that includes a detergent. The biological sample can then be tested for the presence of particular nucleic acid species using in vitro amplification. The method can improve detection of some target nucleic acids without substantially compromising the detection of others. The method is particularly useful for simultaneously preparing RNA and DNA templates for use in multiplex amplification reactions.


Intel has been awarded US Patent No. 8,070,928, "Nanofabricated structures for electric field-assisted nucleic extraction."

Steven Sundberg, Xing Su, and Grace Credo are named as inventors on the patent.

Provides devices and methods for extracting nucleic acid molecules from solution using electric fields. The structures and methods described are suited to incorporation into micro- and nanofluidic devices, such as lab-on-a-chip devices and micro total analysis systems.


Kaohsiung Medical University has been awarded US Patent No. 8,067,568, "Method for diagnosing spinal muscular atrophy."

Shou-Mei Wu, Chun-Chiu Wang, Jan-Gowth Chang, and Yuh-Jyh Jong are named as inventors on the patent.

The described method includes providing a biological sample of a subject containing a nucleotide of the SMN gene; amplifying SMN exons 1, 2a, 2b, 3, 4, 5, 6, 7, and 8 by a universal multiplex PCR using the nucleotide as a template and appropriate primers; labeling the fragments of the SMN exons with a fluorescent primer to obtain fluorescence-labeled exon fragments; and analyzing the fluorescence-labeled exon fragments by capillary electrophoresis. If the SMN1/SMN2 ratios in exon 7 and 8 are different, it indicates that the subject is susceptible to spinal muscular atrophy. Additionally, if the peak of certain exon fragment appears crossed, it indicates an intragenic mutation in the exon, the patent's abstract states.


MicroFluidic Systems (PositiveID) has been awarded US Patent No. 8,053,214, "Apparatus and method of extracting and optically analyzing an analyte from a fluid-based sample."

Allen Northrup is named as inventor on the patent.

Describes an extraction and analysis device that includes a microfluidic-based collection system that extracts one or more different analytes from a fluid-based sample; and an optical analysis system directly coupled to the collection system to perform optical analysis on the collected analytes. The collection system includes microfluidic circuitry for directing a fluid-based sample to a purification chip. Analytes collected within the chip can be either subsequently removed and analyzed or analyzed directly in the purification chip using the optical analysis system. The chip is preferably composed of a plurality of pillars, with the surface area of each pillar coated with a specific capture chemistry … such that a ligand, such as a nucleic acid, an aptamer, or antibody, is attached to each pillar.

The Scan

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CRISPR for What Ails You

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Nature Papers Review Integration of Single-Cell Assay Data, Present Approach to Detect Rare Variants

In Nature this week: review of ways to integrate data from single-cell assays, and more.